Tried out a Canon T3i today with the StackShot. Unfortunately, I do not yet have a macro lens for this camera, so I used a telephoto lens with a Raynox 250 on it. The spider is really old and has been sitting around for a long time. The lighting was just the built in flash bounced off of a sheet of paper. The lens was a Canon EF 75-300mm F/4-5.6 III. The Raynox was 200 mm from the sensor.

The file size of my images seem small for 18 MP. Do I have a setting wrong somewhere? Each image is between 4 and 7 Mb. BTW, why is each image a different filesize in the first place??? I took some through the Raynox in the field and they are about 3.8 Mb and some action sports shots I took with a telephoto are around 7.0 Mb.

The size sounds reasnable for compressed images. The actual number of bytes will depend on the image because there's less information to store from eg a plain background.
I daresay the camera can "do" other formats. If it'll do tiff, those go straight into Zerene. I see a few tiny differences between highest quality jpeg and tiff derived images. These are generally in the parts of the image which get repaired by retouching though, such as in glares and flares. Zerene sees the jpeg detail as worth keeping!

Chris is right about the jpeg compression changes. Any difference in the photo will give different compression requirements and affect the final file size. Also, since I presume you're shooting straight jpegs, that camera has a lot of different file size and aspect ratio choices. If you've played with any of the settings between shots (which I doubt since they're buried in the options menus) that could do it too, although I'm not sure the stack would work if you did that. If you shoot raw, all the files will be the same size. Bigger, but all the same. You can convert the raws to tiffs to stack in ZS. I almost never use jpegs and sRGB color unless I'm emailing or posting them. But that's just me. I have an issue with spending a ton of money on a nice camera sensor then trashing a huge amount of image data before I even save the file! I'd rather process the file first, get what I want, then convert to tiff/ProPhoto RGB or jpeg/sRGB. Admitedly though, that might be overkill for this kind of stacking.

Give or take a little, anyway. Canon raw files are compressed (without loss), so their length does vary some depending on image characteristics. In the list of .CR2's that I'm looking at right now, there are files from 15,183 KB up to 18,942 KB.

I know that it'll do RAW, but I'm not a big fan of RAW when stacking. I think I have to improve my technique before I worry about RAW versus jpeg.

I've tried this setup in the field, but didn't have any luck getting the focal plane right. How about the quality of the stack? Did it come out ok?

When I do this setup with the Raynox on a telephoto, can I use it anywhere in the telephoto's range? Or is the Raynox like a microscope objective and needs to be a particular distance from the sensor? Does the telephoto need to be focused at infinity?

I do almost all my stacks as JPEG too, simply because for bench work it's a lot quicker and the quality loss is quite small.

Raynox lenses are very tolerant of focus. You can use it anywhere in the telephoto's focus range. If the telephoto is zoom, you can also adjust the zoom setting, at least up to whatever point the Raynox starts vignetting.